PLUMED-NEST

Project ID: plumID:20.017
Source: beaded-helix/helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.plumed.dat
Originally used with PLUMED version: 2.7
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr

Click on the labels of the actions for more information on what each action computes

#UNITS LENGTH=A TIME=fs ENERGY=kcal/mol

b1: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1
b2: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=12
cas: 
GROUP
Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms. More details
 
ATOMS
the numerical indexes for the set of atoms in the group
=1-12

dend: 
DISTANCE
Calculate the distance between a pair of atoms. More details
 
ATOMS
the pair of atom that we are calculating the distance between
=b1,b2
The DISTANCE action with label dend calculates a scalar quantityrg: 
GYRATION
Calculate the radius of gyration, or other properties related to it. More details
 
TYPE
 The type of calculation relative to the Gyration Tensor you want to perform
=RADIUS 
ATOMS
the group of atoms that you are calculating the Gyration Tensor for
=cas
en: 
ENERGY
Calculate the total potential energy of the simulation box. More details
 

#The conversion factor is 69.4786 pN = 1 kcal/mol/Angstrom

#0 pN to 100 pN
f: 
FISST
Compute and apply the optimal linear force on an observable to enhance sampling of conformational distributions over a range of applied forces. More details
 
MIN_FORCE
Minimum force (per CV) to use for sampling
=-2.0 
MAX_FORCE
Maximum force (per CV) to use for sampling
=8.0 
PERIOD
Steps corresponding to the learning rate
=200 
NINTERPOLATE
Number of grid points on which to do interpolation
=31 
ARG
the input for this action is the scalar output from one or more other actions
=dend 
OUT_RESTART
Output file for all information needed to continue FISST simulation
=helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.restart.txt 
OUT_OBSERVABLE
Output file putting weights needed to compute observables at different force values
=helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.observable.txt 
OBSERVABLE_FREQ
=1000 
CENTER
 The CV value at which the applied bias energy will be zero
=0 
KBT
The system temperature in units of KB*T
=1

The FISST action with label f calculates the following quantities:
 Quantity   
 Description  
f.bias
the instantaneous value of the bias potential
f.force2
squared value of force from the bias
f._fbar
For each named CV biased, there will be a corresponding output CV_fbar storing the current linear bias prefactor
PRINT
Print quantities to a file. More details
 
ARG
the input for this action is the scalar output from one or more other actions
=dend,rg,en,f.dend_fbar,f.bias,f.force2 
FILE
the name of the file on which to output these quantities
=helix_fisst_fmin-2.0_fmax8.0_eps7.5_10000000.en.colvar.txt 
STRIDE
 the frequency with which the quantities of interest should be output
=5000